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Sample GSM120890 Query DataSets for GSM120890
Status Public on Nov 08, 2006
Title Case_19_2005061504
Sample type genomic
 
Channel 1
Source name control DNA
Organism Homo sapiens
Characteristics normal individual, Tissue : lymphocyte
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from lymphocytes of normal individuals.
Label Cy5
Label protocol The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy5-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.
 
Channel 2
Source name 68/F Rectum
Organism Homo sapiens
Characteristics Age: 68, Gender: female, tissue : rectum
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from a frozen fragment of the tumor, using a microdissection technique to reduce contamination with non-neoplastic tissue. DNA was extracted using a standard proteinase K digestion followed by phenol/chloroform extraction and ethanol precipitation.
Label Cy3
Label protocol The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy3-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.
 
 
Hybridization protocol Probe preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (200 pmol) of Cy5- and Cy3-labeled probe were combined with 100 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 400 ug yeast tRNA to hybridize a spotting area of 24 x 60 mm. The slide was blocked with 50 ug Cot-1 DNA and 300 ug salmon sperm DNA dissolved in 60 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75C. Blocking solution was then placed on the slide covered with a coverslip (24 x 60 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 60 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.
Scan protocol Array slides were scanned with a GenePix 4000B scanner and hybridization signals were evaluated using GenePixPro 3.0 image analysis software.
Description Comparison between individual with Gastrointestinal stromal tumor (GIST) vs normal individual
Data processing All data analysis was performed with Excel. Spot intensities were corrected for local background, and only spots with signal intensities at least two fold above background signal intensities were included in the final analysis. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes followed by the 2D normalization. Normalized ratios of the duplicates were averaged and a log2 value was calculated. Precise localizations of clones spotted on the array were obtained from the Ensemble database (www.ensembl.org/Homo_sapiens). The Normalized ratio is not included in the submitted raw data.
 
Submission date Jul 18, 2006
Last update date Nov 08, 2006
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL3892
Series (1)
GSE5336 Array CGH Analysis in primary gastrointestinal stromal tumors

Data table header descriptions
ID_REF
X the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm - Cy5).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm - Cy5).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm - Cy5).
B635 Median the median feature background intensity at wavelength #1 (635 nm - Cy5).
B635 Mean the mean feature background intensity at wavelength #1 (635 nm - Cy5).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm - Cy5).
% > B635+1SD
% > B635+2SD
F635 % Sat. the percentage of feature pixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm - Cy3).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm - Cy3).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm - Cy3).
B532 Median the median feature background intensity at wavelength #2 (532 nm - Cy3).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm - Cy3).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm - Cy3).
% > B532+1SD
% > B532+2SD
F532 % Sat. the percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R? the coefficient of determination for the current regression value.
F Pixels the total number of feature pixels.
B Pixels the total number of background pixels.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
VALUE Log Ratio = log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at wavelength #2 with the median background subtracted.
Flags the type of flag associated with a feature.

Data table
ID_REF X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1 2340 2200 130 2630 2610 713 753 780 269 100 98 0 1772 1794 378 554 561 136 100 100 0 0.649 0.668 0.673 0.693 1.512 0.626 0.777 120 940 3095 3097 null 1877 1218 1857 1240 0
2 2730 2200 180 851 895 348 754 769 255 30 12 0 710 725 173 608 621 142 38 14 0 1.052 0.83 0.582 0.564 3.879 0.076 0.01 256 1924 199 258 null 97 102 141 117 -50
3 3130 2200 180 973 988 320 849 989 2200 0 0 0 785 795 179 663 919 3421 0 0 0 0.984 0.95 0.707 0.68 5.188 1.632 0.807 256 1924 246 271 null 124 122 139 132 -50
4 3520 2200 120 2885 2920 572 966 999 347 99 99 0 2496 2547 468 704 737 250 100 100 0 0.934 0.943 0.952 0.956 1.437 0.898 0.776 120 820 3711 3797 null 1919 1792 1954 1843 0
5 3930 2200 120 1799 1805 380 722 756 279 99 89 0 1441 1423 254 664 679 231 98 86 0 0.721 0.701 0.694 0.716 1.625 0.625 0.591 120 820 1854 1842 null 1077 777 1083 759 0
6 4330 2200 130 1512 1609 511 615 631 230 95 87 0 1439 1495 329 597 611 142 100 100 0 0.939 0.903 0.889 0.986 1.914 0.778 0.565 120 940 1739 1892 null 897 842 994 898 0
7 4740 2200 130 1477 1486 395 621 636 230 95 83 0 1170 1184 219 582 589 132 98 93 0 0.687 0.696 0.666 0.711 2.038 0.556 0.456 120 940 1444 1467 null 856 588 865 602 0
8 5140 2200 120 887 943 314 591 615 227 65 30 0 960 980 208 587 593 132 91 70 0 1.26 1.116 1.08 1.153 3.069 0.648 0.176 120 820 669 745 null 296 373 352 393 0
9 5540 2170 80 940 907 262 605 633 248 59 25 0 863 859 158 626 641 155 73 30 0 0.707 0.772 0.872 0.876 3.585 0.242 0.075 52 340 572 535 null 335 237 302 233 0
10 5950 2200 130 2188 2208 697 588 615 251 99 95 0 1990 1986 386 606 623 153 100 100 0 0.865 0.852 0.861 0.913 1.552 0.785 0.785 120 940 2984 3000 null 1600 1384 1620 1380 0
41 2330 2600 130 1824 1861 469 753 765 267 99 90 0 1341 1343 231 517 523 124 100 99 0 0.769 0.745 0.746 0.783 1.663 0.613 0.59 120 940 1895 1934 null 1071 824 1108 826 0
42 2730 2600 130 2444 2390 699 727 754 276 100 94 0 2020 2036 494 566 579 164 100 100 0 0.847 0.884 0.91 0.926 1.494 0.829 0.789 120 940 3171 3133 null 1717 1454 1663 1470 0
43 3150 2600 110 1235 1242 359 808 833 273 61 37 0 1066 1051 194 584 597 138 95 82 0 1.129 1.076 0.859 1.159 3.258 0.525 0.167 80 656 909 901 null 427 482 434 467 0
44 3530 2600 180 957 976 277 844 865 297 27 4 0 768 770 185 642 656 147 42 18 0 1.115 0.97 0.657 0.702 3.861 0.057 0.004 256 1924 239 260 null 113 126 132 128 -50
45 3930 2600 120 2337 2352 654 672 696 275 100 99 0 2219 2228 563 626 645 204 100 100 0 0.957 0.954 0.95 0.965 1.454 0.933 0.808 120 820 3258 3282 null 1665 1593 1680 1602 0
46 4330 2600 120 1870 1929 514 633 660 242 99 96 0 1460 1485 315 629 640 147 100 98 0 0.672 0.66 0.667 0.662 1.573 0.594 0.698 120 820 2068 2152 null 1237 831 1296 856 0
47 4740 2600 160 1790 1888 641 619 629 226 99 92 0 2110 2247 708 602 612 136 99 99 0 1.288 1.296 1.315 1.362 1.626 1.239 0.758 208 1512 2679 2914 null 1171 1508 1269 1645 0
48 5130 2600 140 1260 1309 445 600 618 228 86 67 0 1132 1180 305 572 581 136 97 89 0 0.848 0.858 0.913 0.968 2.194 0.711 0.544 156 1140 1220 1317 null 660 560 709 608 0
49 5530 2590 150 1284 1359 514 570 603 240 84 72 0 1197 1228 313 566 585 177 96 83 0 0.884 0.839 0.846 0.918 2.351 0.703 0.547 156 1272 1345 1451 null 714 631 789 662 0
50 5930 2590 150 3282 3481 1151 597 607 236 100 100 0 3977 4155 1130 583 601 205 100 100 0 1.264 1.239 1.281 1.273 1.36 1.237 0.914 156 1272 6079 6456 null 2685 3394 2884 3572 0

Total number of rows: 3840

Table truncated, full table size 654 Kbytes.




Supplementary data files not provided
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